Introduction to ImageJ/Fiji Coding for Image Processing and Analysis

This workshop is designed for geoscientists with a vested interest in extracting maximum value from rock imaging. The objective is to provide a foundational framework of image processing and analysis and the skill to translate that understanding into scientifically-robust, clean, and reproducible code for single and batch image processing. ImageJ/Fiji is the lingua franca due to its user-friendly GUI and the ease of coding, particularly for those new to coding. The knowledge and skills gained in this course will enable participants to supercharge their analytical pipelines as well as serve as a stepping stone towards more powerful coding languages such as Python.

This workshop will follow the 'flipped classroom' paradigm where the attendees will peruse provided materials, with the workshop serving as an active discussion of the material. Furthermore, the workshop is hands-on with scripting being performed in real-time on images of the attendees choice. The workshop will begin at 1pm local time in London. Estimated duration is 4 hrs (max). This is a physical event only. No remote attendance. This workshop is open for all RISIG members. Attendance is FREE. Registration is required as numbers are limited.

There will be a coffee break half way through the afternoon.

Agenda

• Welcome and Introductions
• Introduction to IMAGEJ/FIJI and Digital Image Analysis (DIA) Fundamentals
• Live Scripting of DIA Pipelines
• Coffee break
• Batch Processing
• Looking beyond FIJI, Summary & Wrap-Up

Presenter

Issac is a final-year Ph.D. candidate based at Texas A&M University, College Station, USA, and its branch campus in Doha, Qatar. His dissertation is focused on segmenting and classifying carbonate components from images, specifically transmitted-light petrography and SEM images, using explainable artificial intelligence. He has conducted this workshop to over 40 graduate students and faculty at both Texas A&M University at Qatar and Norwegian University of Science and Technology (NTNU), as part of IRIS-2022. He has also recently been certified as an Evidence-based STEM tutor by the Center for Integration of Research, Teaching, and Learning (CIRTL) network.